Section 5. Next Generation Sequencing You have the option of three experimental

Question

Section 5. Next Generation Sequencing  

You have the option of three experimental technologies to interrogate your sample.

Option 1 – Next Generation whole genome sequencing technology with 100 million reads (human)

Option 2 – Affymetrix SNP microarray chip for known human variants

For each of the above technology options, identify advantages and disadvantages when the technologies are used to identify a set of known SNPs.

For each of the above technology options, identify advantages and disadvantages when the technologies are used to locate and quantify unknown SNPs in a specific chromosome.

Creative answer – What would the results describe if your sample were from a mouse with all other inputs and conditions the same?

Explanation / Answer

1. If one needs to identify translocations,deletions,mosasisims one needs to use next gen whole genome sequencing as this technique would give an information about the sequence of various genes present in the sample compared to SNP chip array. Whole genome sequencing can very wel identify the SNP present in mitochondria as well as promoters.

The read that one gets from WGS is huge and becomes difficult to evaluate the repetitive sequences, whereas SNP chips can precisely help us to identify the SNP as the chip contains DNA of repetitive sequences as well.

2. WGS can be used to identify translocations, deletions etc. WGS data will be huge and the analysis part is time consuming due to repetitive DNA that might be present in the sample.WGS can definitely help us to determine the location of SNP if analysis is done precisely. On the other hand SNP chip array would not be helpful to determine new SNPs as the SNP within the chip is fixed.

3. If the sample would have been from a mouse, one would clearly see 33 % homology between the entire genome. Also number of repetitive DNA is less, and the data that needs to be analysed becomes slightly more easier.

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